Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Out of memory error in GetPileupSummaries



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    Gökalp Çelik

    Hi Mynn

    Looks like you are trying to run this command under WSL1 which is not a supported environment for our tools. Memory management and code execution is not like a native linux environment therefore we recommend you to shift your environment to docker or try converting your WSL environment to version 2 which uses a Hyper-V VM for the linux subsystem. Beware that WSL2 has separate memory settings that may need further configuration for you to modify to make sure that WSL2 can use as much memory as you want. The default configuration is always half the total system memory size. 

    Yet again this may not provide you a proper environment since windows and linux subsystem is not a supported environment for GATK. 


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    Hi Gökalp

    Thank you for a quick and kind response. So it seems that it was a compatibility issue between systems. Since I cannot setup a dedicated Linux workstation right now, I would have to resort to WSL2 with appropriate memory configuration as you recommended and see if it works. I will let the team know if I run into additional problems.

    Thank you for your professional help!

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